def showTable(self, frame, model, label=''):
"""Show model in table"""
tf = LabelFrame(frame, text=label)
tf.pack(fill=BOTH, expand=1)
mtable = TableCanvas(tf, model=model, cellwidth=70, editable=False)
mtable.createTableFrame()
return mtable
def showTable(self, frame, model, label=''):
"""Show model in table"""
tf=LabelFrame(frame,text=label)
tf.pack(fill=BOTH,expand=1)
mtable = TableCanvas(tf, model=model, cellwidth=70,
editable=False)
mtable.createTableFrame()
return mtable
def loadTable(self, dictdata=None, model=None):
if model != None:
self.model = model
else:
self.model = DictModel(dictdata)
self.model.setSortOrder(0)
self.table = TableCanvas(self.tframe, self.model)
self.table.createTableFrame()
return
def __init__(self, parent=None, model=None, width=250,height=100):
TableCanvas.__init__(self, parent, model, width=width,height=height)
self.cellwidth=50
self.rowheight=18
self.thefont = "Arial 10"
self.cellbackgr = 'white'
self.autoresizecols = 1
self.parent = parent
return
def __init__(self, parent=None, model=None, width=250, height=100):
TableCanvas.__init__(self, parent, model, width=width, height=height)
self.cellwidth = 50
self.rowheight = 18
self.thefont = "Arial 10"
self.cellbackgr = 'white'
self.autoresizecols = 1
self.parent = parent
return
def viewAll(self, parent=None):
"""Display all meta data in a table"""
from PEATDB.Tables import TableCanvas
from PEATDB.TableModels import TableModel
tp = Toplevel(master=parent)
tframe = Frame(tp)
tframe.pack()
m = TableModel()
m.importDict(self.data)
table = TableCanvas(tframe, model=m)
table.createTableFrame()
return
def viewAll(self, parent=None):
"""Display all meta data in a table"""
from PEATDB.Tables import TableCanvas
from PEATDB.TableModels import TableModel
tp = Toplevel(master=parent)
tframe = Frame(tp)
tframe.pack()
m = TableModel()
m.importDict(self.data)
table = TableCanvas(tframe, model=m)
table.createTableFrame()
return
def loadTable(self, dictdata=None, model=None):
if model != None:
self.model = model
else:
self.model = DictModel(dictdata)
self.model.setSortOrder(0)
self.table = TableCanvas(self.tframe, self.model)
self.table.createTableFrame()
return
def updateJobsTable(self):
"""Show table for current jobs list"""
self.checkJobsDict()
jobdict = self.DB.meta.peatsa_jobs
M = TableModel()
#open job log from file
f = open('jobstates.log', 'r')
jl = pickle.load(f)
for j in jobdict:
jobid = jobdict[j]
try:
M.addRecord(j,
state=jl[jobid]['State'],
date=jl[jobid]['Date'])
except:
M.addRecord(j, state='Not in DB')
self.jobstable = TableCanvas(self.tf,
model=M,
height=100,
editable=False)
self.jobstable.createTableFrame()
self.log.yview('moveto', 1)
f.close()
return
def updateJobsTable(self):
"""Show table for current jobs list"""
self.checkJobsDict()
jobdict = self.DB.meta.peatsa_jobs
M = TableModel()
#open job log from file
f=open('jobstates.log','r')
jl = pickle.load(f)
for j in jobdict:
jobid = jobdict[j]
try:
M.addRecord(j,state=jl[jobid]['State'],date=jl[jobid]['Date'])
except:
M.addRecord(j,state='Not in DB')
self.jobstable = TableCanvas(self.tf, model=M, height=100, editable=False)
self.jobstable.createTableFrame()
self.log.yview('moveto', 1)
f.close()
return
def __init__(self, parent=None, model=None, width=300,height=100):
TableCanvas.__init__(self, parent, model, width=width,height=height)
self.parent = parent
return
def createTableFrame(self):
TableCanvas.createTableFrame(self)
self.drawInactive()
return
class DictEditor(Frame, GUI_help):
"""Simple app to allow edit/save dicts in table"""
def __init__(self, parent=None):
self.parent = parent
if not self.parent:
Frame.__init__(self)
self.main=self.master
else:
self.main=Toplevel()
self.main.title('Dict Editor')
self.main.geometry('600x600+200+200')
bf=Frame(self.main)
bf.pack(side=RIGHT)
Button(bf,text='Load Pickle',command=self.loadDict).pack(side=TOP,fill=X)
Button(bf,text='Save',command=self.saveDict).pack(side=TOP,fill=X)
Button(bf,text='Import CSV',command=self.loadCSV).pack(side=TOP,fill=X)
Button(bf,text='Save as CSV',command=self.saveCSV).pack(side=TOP,fill=X)
Button(bf,text='Add Row',command=self.addRow).pack(side=TOP,fill=X)
Button(bf,text='Quit',command=self.quit).pack(side=TOP,fill=X)
self.tframe=Frame(self.main)
self.tframe.pack(side=LEFT,expand=1,fill=BOTH)
self.filename = None
self.table=None
return
def loadDict(self, filename=None):
if filename==None:
import tkFileDialog
filename=tkFileDialog.askopenfilename(defaultextension='.pickle',
filetypes=[("pickle","*.pickle"),
("All files","*.*")],
parent=self.main)
if filename != None:
self.dictdata = pickle.load(open(filename,'r'))
self.loadTable(self.dictdata)
self.filename = filename
return
def saveDict(self):
"""Pickle dict from table contents"""
if self.table == None:
return
if self.filename == None:
import tkFileDialog
self.filename=tkFileDialog.asksaveasfilename(defaultextension='.pickle',
filetypes=[("pickle","*.pickle"),
("All files","*.*")],
parent=self.main)
pickle.dump(self.model.data,open(self.filename,'w'))
return
def loadCSV(self):
"""Load a csv file as a dict and display"""
from PEATDB.IO import Importer
IM = Importer()
IM.getLines()
IM.showimportDialog()
self.wait_window(IM.ask_csv)
model = DictModel()
model.importDict(IM.data)
self.filename=None
self.loadTable(model=model)
return
def saveCSV(self):
"""Export csv from table contents"""
if self.filename == None:
return
self.table.exportTable()
return
def loadTable(self, dictdata=None, model=None):
if model != None:
self.model = model
else:
self.model = DictModel(dictdata)
self.model.setSortOrder(0)
self.table = TableCanvas(self.tframe, self.model)
self.table.createTableFrame()
return
def addRow(self):
"""add a row"""
if self.table == None:
return
self.table.add_Row()
return
def quit(self):
self.main.destroy()
return
class DictEditor(Frame, GUI_help):
"""Simple app to allow edit/save dicts in table"""
def __init__(self, parent=None):
self.parent = parent
if not self.parent:
Frame.__init__(self)
self.main = self.master
else:
self.main = Toplevel()
self.main.title('Dict Editor')
self.main.geometry('600x600+200+200')
bf = Frame(self.main)
bf.pack(side=RIGHT)
Button(bf, text='Load Pickle', command=self.loadDict).pack(side=TOP,
fill=X)
Button(bf, text='Save', command=self.saveDict).pack(side=TOP, fill=X)
Button(bf, text='Import CSV', command=self.loadCSV).pack(side=TOP,
fill=X)
Button(bf, text='Save as CSV', command=self.saveCSV).pack(side=TOP,
fill=X)
Button(bf, text='Add Row', command=self.addRow).pack(side=TOP, fill=X)
Button(bf, text='Quit', command=self.quit).pack(side=TOP, fill=X)
self.tframe = Frame(self.main)
self.tframe.pack(side=LEFT, expand=1, fill=BOTH)
self.filename = None
self.table = None
return
def loadDict(self, filename=None):
if filename == None:
import tkFileDialog
filename = tkFileDialog.askopenfilename(defaultextension='.pickle',
filetypes=[
("pickle", "*.pickle"),
("All files", "*.*")
],
parent=self.main)
if filename != None:
self.dictdata = pickle.load(open(filename, 'r'))
self.loadTable(self.dictdata)
self.filename = filename
return
def saveDict(self):
"""Pickle dict from table contents"""
if self.table == None:
return
if self.filename == None:
import tkFileDialog
self.filename = tkFileDialog.asksaveasfilename(
defaultextension='.pickle',
filetypes=[("pickle", "*.pickle"), ("All files", "*.*")],
parent=self.main)
pickle.dump(self.model.data, open(self.filename, 'w'))
return
def loadCSV(self):
"""Load a csv file as a dict and display"""
from PEATDB.IO import Importer
IM = Importer()
IM.getLines()
IM.showimportDialog()
self.wait_window(IM.ask_csv)
model = DictModel()
model.importDict(IM.data)
self.filename = None
self.loadTable(model=model)
return
def saveCSV(self):
"""Export csv from table contents"""
if self.filename == None:
return
self.table.exportTable()
return
def loadTable(self, dictdata=None, model=None):
if model != None:
self.model = model
else:
self.model = DictModel(dictdata)
self.model.setSortOrder(0)
self.table = TableCanvas(self.tframe, self.model)
self.table.createTableFrame()
return
def addRow(self):
"""add a row"""
if self.table == None:
return
self.table.add_Row()
return
def quit(self):
self.main.destroy()
return
class PEATSAPlugin(Plugin):
"""Template GUI plugin for PEAT App"""
capabilities = ['gui']
requires = ['PEATSA']
menuentry = 'PEATSA Plugin'
gui_methods = {'fetchJob':'Fetch Job from Server',
'editConfigFile' : 'Configure Server',
'help':'Help',
'quit':'Close Window'}
buttonorder = ['createJobDialog','fetchJob','editConfigFile','help','quit']
about = 'This plugin allows you to call PEATSA'
calctypes = ['stability','binding','pka']
def main(self, parent=None, DB=None):
if parent == None:
if DB != None:
self.DB = DB
self.setupConnection()
else:
return
else:
self.parent = parent
self.DB = parent.DB
if self.DB == None:
self.displayNoDBWarning()
return
self._doFrame()
self.setupConnection()
print 'Updating jobs table..'
self.updateJobs()
return self
def setupConnection(self):
"""Set up connection"""
homepath = os.path.expanduser("~")
self.confpath = os.path.join(homepath, 'peatsa.conf')
if os.path.exists(self.confpath):
configuration = Core.Environment.Configuration(filename=self.confpath)
else:
configuration = Core.Environment.Configuration(searchDefaultLocations=False)
configuration.add_section('DATABASE')
configuration.set('DATABASE', 'database', 'DBSAInterface')
configuration.set('DATABASE', 'host', 'enzyme.ucd.ie')
configuration.set('DATABASE', 'user', 'peatdb')
configuration.set('DATABASE', 'password', '123')
configuration.writeToFile(self.confpath)
if self.parent != None:
tkMessageBox.showwarning("Connection Error",
'No PEATSA server configured, press configure server'
' to set a server, username and password.')
self.connect(configuration)
return
def _doFrame(self):
self.mainwin = self.parent.createChildFrame(width=460,title='PEATSA Plugin')
#self.mainwin = self.parent.create
methods = self._getmethods()
methods = [m for m in methods if m[0] in self.gui_methods.keys()]
l=Label(self.mainwin, text='PEATSA Interface')
l.pack(side=TOP,fill=BOTH)
self.tf=LabelFrame(self.mainwin,text='Project Calculations')
self.tf.pack(side=TOP,fill=BOTH,expand=1)
self.manageJobsButtons(self.mainwin)
self._createButtons(methods)
self.log = self.createLogWin(self.mainwin)
self.log.pack(side=TOP,fill=BOTH,expand=1)
self.stdout2Log()
self.mainwin.bind("<Destroy>", self.quit)
#self.parent.sidepane.bind("<Destroy>", self.test1)
return
def _createButtons(self, methods):
"""Dynamically create buttons for supplied methods, which is a tuple
of (method name, label)"""
mbutton=Menubutton(self.mainwin, text='Options', width=12,
borderwidth=2, relief=RIDGE,
activeforeground='red')
menu=Menu(mbutton,tearoff=0)
mbutton['menu']=menu
mbutton.pack(side=BOTTOM,fill=BOTH)
for m in methods:
menu.add_radiobutton(label=self.gui_methods[m[0]],
indicatoron=0,
command=m[1])
b=Button(self.mainwin,text='Create Calculation',command=self.createJobDialog)
b.pack(side=BOTTOM,fill=BOTH)
return
def updateJobsTable(self):
"""Show table for current jobs list"""
self.checkJobsDict()
jobdict = self.DB.meta.peatsa_jobs
M = TableModel()
#open job log from file
f=open('jobstates.log','r')
jl = pickle.load(f)
for j in jobdict:
jobid = jobdict[j]
try:
M.addRecord(j,state=jl[jobid]['State'],date=jl[jobid]['Date'])
except:
M.addRecord(j,state='Not in DB')
self.jobstable = TableCanvas(self.tf, model=M, height=100, editable=False)
self.jobstable.createTableFrame()
self.log.yview('moveto', 1)
f.close()
return
def manageJobsButtons(self, parent):
fr1 = Frame(parent)
Button(fr1,text='View Results',command=self.showAllResults,bg='#ccFFFF').pack(side=TOP,fill=BOTH,expand=1)
fr1.pack(fill=BOTH)
Button(fr1,text='Merge Results',command=self.mergeCurrent).pack(side=TOP,fill=BOTH,expand=1)
fr1.pack(fill=BOTH)
fr = Frame(parent)
c='#ADD8E6'
Button(fr,text='Show Details',command=self.viewDetails,bg=c).pack(side=LEFT,fill=BOTH,expand=1)
Button(fr,text='Manage Results',command=self.manageResults,bg=c).pack(side=LEFT,fill=BOTH,expand=1)
Button(fr,text='Remove',command=self.removeJob,bg=c).pack(side=LEFT,fill=BOTH,expand=1)
Button(fr,text='Resubmit',command=self.resubmitJob,bg=c).pack(side=LEFT,fill=BOTH,expand=1)
fr.pack(fill=BOTH)
return
def createLogWin(self, parent):
log = Pmw.ScrolledText(parent,
borderframe=1,
labelpos = 'n',
label_text='Log',
usehullsize = 1,
hull_width = 800,
hull_height = 200,
text_wrap='word')
return log
def stdout2Log(self):
"""Redirect stdout to app control"""
sys.stdout = self
sys.stderr = self
return
def log2Stdout(self):
"""return to stdout"""
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
return
def write(self, txt):
"""Handle stdout if required"""
self.log.appendtext(txt)
self.log.update_idletasks()
return
def flush(self):
return
def connect(self, configuration):
"""Create connection"""
self.connection = PEATSA.WebApp.UtilityFunctions.ConnectionFromConfiguration(configuration)
self.jobManager = PEATSA.WebApp.Data.JobManager(self.connection)
self.jobManager.setJobStateLogging('jobstates.log',interval=60)
print '\nConnection to server made sucessfully.\n'
return
def createMutationList(self, filename=None):
self.mutationList = Core.Data.MutationListFile(create=False)
return
def fetchJob(self):
"""Get job from it's db ID and add to list"""
mpDlg = MultipleValDialog(title='Get Job',
initialvalues=('','my job1'),
labels=('ID','Your label',),
types=('string','string'),
parent=self.mainwin)
if mpDlg.result == True:
jobid = mpDlg.results[0]
name = mpDlg.results[1]
else:
return
job = PEATSA.WebApp.Data.Job(jobid, self.connection)
if job != None:
print 'adding job id %s to list' %job.identification
self.storeJob(name, job)
self.updateJobs()
return
def writetempPDB(self,name=None,pdbfile='refprot.pdb'):
if name==None:
name = self.DB.meta.refprotein
pdblines = self.DB[name].Structure
#pdbfile = 'refprot.pdb'
fd=open(pdbfile,'w')
for line in pdblines:
fd.write(line)
fd.close()
return pdbfile
def getrefPDBName(self):
name = self.DB.meta.refprotein
if self.DB[name].has_key('pdbname'):
name = self.DB[name]['pdbname']
return name.split('.')[0]
else:
return ''
def createJobDialog(self):
"""Get details from user using dialog
required: structure, mutations, type of calc and a tag (optional)"""
def validatename(text):
if not hasattr(self.DB.meta,'peatsa_jobs'):
return 1
if text in self.DB.meta.peatsa_jobs:
return -1
else:
return 1
def close():
jobdlg.destroy()
def loadmuts():
filename=tkFileDialog.askopenfilename(initialdir=os.getcwd(),
filetypes=[("All files","*")])
if filename:
mutlist.importfile(filename)
return
def loadmutsfromDB():
for p in self.DB.getRecs():
mut = self.DB.get(p).Mutations
if mut == None or mut=='':
continue
if type(mut) is types.StringType:
mutlist.appendtext(mut+'\n')
else:
mutstring = mut.getMutationString()
if mutstring != None:
mutlist.appendtext(mutstring+'\n')
return
def getstruct():
filename=tkFileDialog.askopenfilename(defaultextension='.pdb',
initialdir=os.getcwd(),
filetypes=[("pdb","*.pdb"),("All files","*.*")])
pdbentry.setvalue(filename)
return
def getligand():
self.ligandfile = tkFileDialog.askopenfilename(defaultextension='.pdb',
initialdir=os.getcwd(),
filetypes=[("mol2","*.mol2"),("All files","*.*")])
def submit():
#if calcmenu.getcurselection() == 'both':
# calcs = ['stability','binding']
if calcmenu.getcurselection() == 'pka':
calcs = ['scan']
else:
calcs = [calcmenu.getcurselection()]
mutationlist = mutlist.getvalue().split('\n')
mutationlist.remove('')
pdbfile=None; pdb = None
quality = mutqualentry.getvalue()
if not hasattr(self.DB.meta, 'refprotein') or self.DB.meta.refprotein == None:
tkMessageBox.showinfo('No ref protein',
'Set a reference (wt) protein first')
return
#if self.useref.get() == 1:
#we use ref pdb by default now
pdbfile = self.writetempPDB()
pdbname = self.getrefPDBName()
if len(mutationlist) == 0 or mutationlist==[u'']:
print 'mutation list is empty'
return
if hasattr(self.DB.meta,'peatsa_jobs') and nameentry.getvalue() in self.DB.meta.peatsa_jobs:
print 'job name already used'
return
name=nameentry.getvalue()
expcol = expcolmenu.getcurselection()
self.submitJob(name=name, pdbname=pdbname,
pdb=pdb, pdbfile=pdbfile,
ligandfile=self.ligandfile,
mutations=mutationlist,
calcs=calcs, mutationquality=quality,
meta={'expcol':expcol,'pdbname':pdbname})
close()
jobdlg = Toplevel()
jobdlg.geometry('+220+220')
jobdlg.title('Create Calculation')
balloon = Pmw.Balloon(jobdlg)
nameentry = Pmw.EntryField(jobdlg,
labelpos = 'w',
label_text = 'Name:',
validate = validatename,
value = 'mycalc')
nameentry.pack(fill=BOTH,expand=1)
balloon.bind(nameentry, 'Calculation name can be anything, but should be unique')
expcols = ['']+self.DB.getSimpleFields()
expcolmenu = Pmw.OptionMenu(jobdlg,
labelpos = 'w',
label_text = 'Exp. col:',
items = expcols,
initialitem = '',
menubutton_width = 8)
expcolmenu.pack(fill=BOTH,expand=1)
balloon.bind(expcolmenu, 'Field with experimental data to compare, optional')
calcmenu = Pmw.OptionMenu(jobdlg,
labelpos = 'w',
label_text = 'Calculation Type:',
items = self.calctypes,
initialitem = 'stability',
menubutton_width = 8)
calcmenu.pack(fill=X,expand=1)
fr=Frame(jobdlg)
fr.pack(fill=X,expand=1)
mutqualentry = Pmw.EntryField(jobdlg,
labelpos = 'w',
label_text = 'Quality:',
validate = validatename,
value = '2.0')
mutqualentry.pack(fill=BOTH,expand=1)
Label(jobdlg,text='Using PDB: '+self.getrefPDBName()).pack(fill=BOTH,expand=1)
self.ligandfile=None
mutlist = Pmw.ScrolledText(jobdlg,
labelpos = 'n',
label_text='Mutations:',
usehullsize = 1,
hull_width = 200,
hull_height = 250,
text_wrap='word')
mutlist.pack(fill=BOTH,expand=1)
Button(jobdlg,text='Load Mutations from Project',command=loadmutsfromDB).pack(fill=X,expand=1)
Button(jobdlg,text='Load Mutations from File',command=loadmuts).pack(fill=X,expand=1)
balloon.bind(mutlist, 'Enter one mutation per line in the form\n A:0003:ALA or A3A')
f=Frame(jobdlg); f.pack(fill=X,expand=1)
Button(f,text='Submit',command=submit).pack(side=LEFT,fill=X,expand=1,pady=2)
Button(f,text='Cancel',command=close).pack(fill=X,expand=1,pady=2)
jobdlg.grab_set()
jobdlg.transient(self.parent)
self.parent.wait_window(jobdlg)
return
def submitJob(self, name='mycalc', pdbname=None, pdb=None, pdbfile=None, ligandfile=None,
mutations=[], calcs=['stability'], mutationquality='2.0', meta={}):
"""Submit job to server"""
if 'scan' in calcs and pdbname==None:
print 'You must provide pdb code for pKa calcs'
return
if pdb==None and pdbfile==None:
return
job = self.jobManager.createJob(pdbId=pdbname, calculations=calcs,
dataTable='Data', metadata=meta,
optionArgs={'--mutationQuality':mutationquality})
if pdb != None:
job.setStructure(pdb)
else:
job.setStructureFromFile(pdbfile)
if 'binding' in calcs:
job.setLigandFromFile(ligandfile)
self.mutationList = Core.Data.MutationListFile(filename='tempmutlist', create=True)
sets=[]
for code in mutations:
if code == '': continue
try:
sets.append(Core.Data.MutationSet(code))
except:
print 'mutation code %s incorrect' %code
for s in sets:
self.mutationList.addMutant(s, autoUpdate=False, ignoreDuplicates=True)
self.mutationList.removeDuplicates(autoUpdate=False)
job.setMutationListFile(self.mutationList)
job.setState('Ready')
self.jobManager.logJobStates('jobstates.log')
#add job to peat database
self.storeJob(name, job)
if self.parent != None:
username = self.parent.username
self.updateJobs()
else:
username = None
self.DB.commit(note='peatsa job',user=username)
print 'job submitted successfully'
return
def resubmitJob(self):
"""Resend a job based on new mutations in DB that are not in job already"""
job, name = self.getJob()
if job == None:
return
DB=self.DB
self.matrices = job.data.allMatrices()
for m in matrices:
matrix=matrices[m]
if matrix==None: return
muts = matrix.mutationCodes()
dbmuts = [DB.get(p).Mutations for p in DB.getRecs()]
newmuts = list(set(dbmuts) - set(muts))
print 'the following mutations in the project are not in the job: %s' %newmuts
'''self.submitJob(name=name,
pdb=pdb, pdbfile=pdbfile,
ligandfile=self.ligandfile,
mutations=newmuts,
calcs=calcs, meta={'expcol':expcol}) '''
self.log.yview('moveto', 1)
return
def getJob(self, name=None):
"""Get job from name"""
if name == None:
name = self.jobstable.get_selectedRecordNames()[0]
if name == None:
return None, name
jobid = self.DB.meta.peatsa_jobs[name]
try:
job = PEATSA.WebApp.Data.Job(jobid, self.connection)
except:
#print 'job not in database'
return None,name
return job, name
def removeJob(self):
"""Remove a job from the db"""
job, name = self.getJob()
answer = tkMessageBox.askyesno("Warning",'Remove this job?')
if answer == False:
return
try:
self.jobManager.deleteJob(job)
except:
print 'job not in database, removing from peat'
del self.DB.meta.peatsa_jobs[name]
self.DB.meta.__p__changed = 1
self.updateJobs()
return
def viewDetails(self, name=None):
job, name = self.getJob()
if job==None:
return
jobmeta = job.metadata()
print
print job.data
print 'details for job %s' %name
print 'job status:',job.state()
print 'submitted on ',job.date
if jobmeta.has_key('pdbname'):
print 'original pdb file:', jobmeta['pdbname']
print 'mutations:', len(job.mutationListFile().mutantList())
print '(this job has id %s)' %job.identification
if job.error() != None:
print 'The job had an error..'
print job.error()['ErrorDescription']
print job.error()['DetailedDescription']
print
self.log.yview('moveto', 1)
return
def addColoredText(self, st, tag, word, fg='black', bg='white'):
"""add a space to the end of the word"""
word = word + " "
st.insert('end', word)
end_index = st.index('end')
begin_index = "%s-%sc" % (end_index, len(word) + 1)
st.tag_add(tag, begin_index, end_index)
st.tag_config(tag, foreground=fg, background=bg)
return
def checkJobsDict(self):
"""Check jobs data structure exists"""
if not hasattr(self.DB.meta,'peatsa_jobs'):
from ZODB.PersistentMapping import PersistentMapping
self.DB.meta.peatsa_jobs = PersistentMapping()
def storeJob(self, name, job):
"""Store job to DB"""
self.checkJobsDict()
self.DB.meta.peatsa_jobs[name] = job.identification
return
def updateJobs(self):
if not hasattr(self.DB.meta,'peatsa_jobs'):
return
self.updateJobsTable()
self.wait=self.mainwin.after(60000, self.updateJobs)
return
def mergeResults(self, job, colname, tablemodel):
"""Merge given job results to tablemodel"""
if job==None:
return
matrices = job.data.allMatrices()
if not colname:
return
nf={'Total':colname}
for m in matrices:
matrix = matrices[m]
if matrix == None: continue
M = self.mergeMatrix(matrix, tablemodel, fields=['Total'], newfields=nf)
return
def mergeCurrent(self):
"""Auto merge selected job results to main table
called from GUI """
job, name = self.getJob()
if job==None:
return
#get field name to use
colname = tkSimpleDialog.askstring("Column name?",
"Name for column:",
initialvalue=name+'_Predictions',
parent=self.mainwin)
M = self.parent.tablemodel
self.mergeResults(job, colname, M)
self.parent.updateTable()
#also send some meta data to peatsa_meta?
'''from Correlation import CorrelationAnalyser
C = CorrelationAnalyser()
cc,rmse = C.getStats(pre,exp)
data.append({'name':p,'rmse':rmse,'cc':cc}) '''
return
def manageResults(self, name=None):
"""Get the results back - we can send the matrix to the main peat
table or put results into a labbook sheet.
Also allow user to merge with an existing table"""
job, name = self.getJob(name)
if job.error() != None:
print 'job had an error, use view details'
elif job.state() == 'Finished':
self.showPEATSAResultsDialog(job, name)
else:
print 'Job is not finished yet.'
return
def editConfigFile(self):
"""Edit config file"""
from PEATDB.textFrame import textFrame
tf = textFrame(parent=self.mainwin,
title='PEATSA Conf file')
tf.load_from_file(self.confpath)
self.parent.wait_window(tf.frame)
#reconnect
configuration = Core.Environment.Configuration(filename=self.confpath)
self.connect(configuration)
return
def showPEATSAResultsDialog(self, job, name):
resdlg = Toplevel()
resdlg.geometry('600x450+300+200')
resdlg.title('PEATSA results '+name)
balloon = Pmw.Balloon(resdlg)
self.currname = name
body = Frame(resdlg)
resdlg.initial_focus = body
body.pack(fill=BOTH,expand=1,padx=5, pady=5)
self.matrices = job.data.allMatrices()
fr=Frame(body)
fr.grid(row=0,column=0,sticky='news',rowspan=2)
for m in self.matrices:
if self.matrices[m] != None:
self.showMatrix(fr,self.matrices[m], m)
self.labboklist = self.parent.labbookSheetsSelector(body)
self.labboklist.grid(row=0,column=1,sticky='news')
bf=Frame(body)
bf.grid(row=1,column=1,sticky='ew')
b=Button(bf,text='Merge into main table', command=lambda: self.mergeTable(main=True))
b.pack(fill=X,expand=1)
balloon.bind(b,'Merge results into main DB table')
b=Button(bf,text='Merge into Selected', command=self.mergeTable)
b.pack(fill=X,expand=1)
balloon.bind(b,'Merge results into an existing labbook table by matching the mutations')
b=Button(bf,text='Create new table', command=self.send2Labbook)
b.pack(fill=X,expand=1)
balloon.bind(b,'Send results to a new sheet in the main labbook')
Button(bf,text='Save as CSV', command=self.saveCSV).pack(fill=X,expand=1)
body.columnconfigure(0,weight=1)
body.rowconfigure(0,weight=1)
return
def showMatrix(self, frame, matrix, label=''):
"""Show matrix in table"""
M = self.matrix2Table(matrix)
mtable = self.showTable(frame, M, label)
return mtable
def showTable(self, frame, model, label=''):
"""Show model in table"""
tf=LabelFrame(frame,text=label)
tf.pack(fill=BOTH,expand=1)
mtable = TableCanvas(tf, model=model, cellwidth=70,
editable=False)
mtable.createTableFrame()
return mtable
def mergeTable(self, main=False):
"""Send a matrix to the peat main table or labbook sheet
by merging matching mutations.
Requires that one field in the table stores compatible
mutant format supported by PEATSA"""
if main == False:
try:
name = self.labboklist.getcurselection()[0]
except:
print 'no name selected'
return
if main == True:
for m in self.matrices:
matrix = self.matrices[m]
if matrix == None: continue
M = self.parent.tablemodel
M = self.mergeMatrix(matrix, M)
self.parent.updateTable()
else:
M = self.DB.getLabbookSheet(name)
for m in self.matrices:
matrix = self.matrices[m]
if matrix == None: continue
M = self.mergeMatrix(matrix, M)
if M != None:
self.DB.createLabbookSheet(name, M)
self.parent.startLabbook('ALL')
return
def send2Labbook(self):
"""Send matrix to selected labbook"""
#get name
cols = ['']+self.DB.getSimpleFields()
DB=self.DB
mpDlg = MultipleValDialog(title='Send to Labbook',
initialvalues=(self.currname, cols),
labels=('table name','exp data column'),
types=('string','list'),
parent=self.mainwin)
if mpDlg.result == False:
return
name = mpDlg.results[0]
expcol = mpDlg.results[1]
M = DBActions.sendDB2Labbook(DB,recs=None,cols=['Mutations',expcol],name=name)
for m in self.matrices:
matrix = self.matrices[m]
if matrix != None:
M = self.mergeMatrix(matrix, M)
self.DB.createLabbookSheet(name, M)
self.parent.startLabbook('ALL')
return
def saveCSV(self):
"""Save matrix to csv"""
filename=tkFileDialog.asksaveasfilename(defaultextension='.csv',
initialdir=os.getcwd(),
filetypes=[("csv","*.csv"),("All files","*.*")])
if not filename:
return
for m in self.matrices:
matrix = self.matrices[m]
if matrix != None:
c=matrix.csvRepresentation()
f=open(filename,'w')
f.write(c)
f.close()
return
def matrix2Table(self, matrix):
"""Creates a table model from a peatsa matrix"""
M = TableModel()
M.addColumn('Mutations')
fields = matrix.columnHeaders()
for f in fields:
M.addColumn(f)
i = matrix.indexOfColumnWithHeader('Mutations')
for row in matrix:
mutationSet = Core.Data.MutationSet(row[i])
code = '+'.join(mutationSet.mutationCodes(reduced=True))
M.addRow(code)
for f in fields:
j = matrix.indexOfColumnWithHeader(f)
if f == 'Mutations':
M.data[code]['Mutations'] = code
else:
M.data[code][f] = str(row[j])
return M
def mergeMatrix(self, matrix, model, fields=None, newfields=None):
"""Merge a peatsa matrix with a table, returns merged tablemodel
tablemodel: input tablemodel
fields: which fields from matrix should be included in merge, default all
newfields: a dict that can map matrix names to new col names
"""
M = self.matrix2Table(matrix)
if fields==None:
fields = M.columnNames
key = 'Mutations'
if not key in model.columnNames:
print 'this table has no mutations column, we cannot merge'
return
i = matrix.indexOfColumnWithHeader(key)
for row in model.reclist:
try:
mset1 = Core.Data.MutationSet(model.data[row][key])
except:
continue
for rec in M.reclist:
try:
mset2 = Core.Data.MutationSet(M.data[rec][key])
except:
continue
if mset1 == mset2:
#add this data to table
for f in fields:
if newfields!=None and newfields.has_key(f):
col = newfields[f]
else:
col = f
if not M.data[rec].has_key(f): continue
model.addColumn(col)
try:
model.data[row][col] = float(M.data[rec][f])
except:
model.data[row][col] = M.data[rec][f]
return model
def showAllResults(self):
"""Show results for single or multiple jobs together"""
names = self.jobstable.get_selectedRecordNames()
if len(names)==1:
ax,mh,x,y=self.showResults()
else:
tx=[]; ty=[]
import pylab as plt
f=plt.figure(figsize=(8,8))
ax=f.add_subplot(111)
for n in names:
a,mh,x,y = self.showResults(n,showtable=False, ax=ax,stats=False)
tx.extend(x)
ty.extend(y)
ax.legend()
#add stats for summary
from Correlation import CorrelationAnalyser
C = CorrelationAnalyser()
C.addStats(ax,tx,ty)
f.show()
return
def showResults(self, name=None, showtable=True, ax=None, stats=True):
"""Show results with correlation plot from selected job"""
job, name = self.getJob(name)
if job == None:
print 'job not in DB'
return
if job.state() != 'Finished':
print 'job not finished'
return
self.matrices = job.data.allMatrices()
#print self.matrices['ModellingResults'].csvRepresentation()
jobmeta = job.metadata()
cols = self.DB.getSimpleFields()
expcol = None
expdata = None
#print jobmeta
if jobmeta.has_key('expcol'):
expcol = jobmeta['expcol']
if expcol not in cols and jobmeta.has_key('project'):
#we may have stored the exp data in another project
prjdata = jobmeta['project']
print 'trying to loading exp data from external project(s)'
from PEATDB.Base import PDatabase
from PEATTables import PEATTableModel
tmpdb = PDatabase(**prjdata)
print tmpdb
S = PEATTableModel(tmpdb)
expdata = S.simpleCopy(include=['Mutations'])
print expdata
#if exp column not known then ask user
if expcol == '' or expcol == None:
mpDlg = MultipleValDialog(title='Select Experimental Data',
initialvalues=[cols],
labels=['exp data column:'],
types=['list'],
parent=self.mainwin)
if mpDlg.result == True:
expcol = mpDlg.results[0]
else:
return
for m in self.matrices:
matrix = self.matrices[m]
if matrix == None or not 'Total' in matrix.columnHeaders():
continue
ax,mh,x,y = self.plotMerged(matrix, expcol, expdata, m,
showtable, ax, name, stats)
#need to add this for mousehandler to work.. hack
'''from Correlation import MouseHandler
mh = MouseHandler(ax, labels=expcol, key='Mutations')
mh.connect()'''
return ax,mh,x,y
def plotMerged(self, matrix, expcol, expdata=None,
title='', showtable=True, ax=None, name=None,
stats=True):
"""Merge a set of exp vals with predictions and plot"""
if expdata==None:
expdata = self.parent.tablemodel.simpleCopy(include=['Mutations'])
merged = self.mergeMatrix(matrix, expdata)
x,y,names,muts = merged.getColumns(['Total',expcol,'name','Mutations'],allowempty=False)
from Correlation import CorrelationAnalyser
C = CorrelationAnalyser()
muts = ['mutation: '+i for i in muts]
labels = zip(names, muts)
ax,frame,mh = C.plotCorrelation(x,y,labels,title=title,ylabel=expcol,
ax=ax,plotname=name,stats=stats,err=4)
x=[round(float(i),2) for i in x]
y=[round(float(i),2) for i in y]
if showtable == True:
table = self.showTable(frame, merged)
mh.table = table
return ax,mh,x,y
def test(self):
job, name = self.getJob('myjob')
if job.error() != None or job.state() != 'Finished':
return
stabmatrix = job.data.stabilityResults
L = self.DB.getLabbookSheet('myjob')
L = self.mergeMatrix(stabmatrix, L, fields=['name'])
print L.columnNames
#L1 = self.DB.getLabbookSheet('myjob3')
#L.merge(L1)
return
def displayNoDBWarning(self):
"""Warn user that no DB is present"""
tkMessageBox.showwarning("Cannot launch plugin",
'No Database is currently open. '
'You should first open a project.')
return
def help(self):
import webbrowser
link='http://enzyme.ucd.ie/main/index.php/PEAT_SA'
webbrowser.open(link,autoraise=1)
return
def quit(self, evt=None):
"""We MUST stop the jobManager"""
self.log2Stdout()
self.jobManager.stopLogging()
self.mainwin.destroy()
print 'closing plugin'
return
class PEATSAPlugin(Plugin):
"""Template GUI plugin for PEAT App"""
capabilities = ['gui']
requires = ['PEATSA']
menuentry = 'PEATSA Plugin'
gui_methods = {
'fetchJob': 'Fetch Job from Server',
'editConfigFile': 'Configure Server',
'help': 'Help',
'quit': 'Close Window'
}
buttonorder = [
'createJobDialog', 'fetchJob', 'editConfigFile', 'help', 'quit'
]
about = 'This plugin allows you to call PEATSA'
calctypes = ['stability', 'binding', 'pka']
def main(self, parent=None, DB=None):
if parent == None:
if DB != None:
self.DB = DB
self.setupConnection()
else:
return
else:
self.parent = parent
self.DB = parent.DB
if self.DB == None:
self.displayNoDBWarning()
return
self._doFrame()
self.setupConnection()
print 'Updating jobs table..'
self.updateJobs()
return self
def setupConnection(self):
"""Set up connection"""
homepath = os.path.expanduser("~")
self.confpath = os.path.join(homepath, 'peatsa.conf')
if os.path.exists(self.confpath):
configuration = Core.Environment.Configuration(
filename=self.confpath)
else:
configuration = Core.Environment.Configuration(
searchDefaultLocations=False)
configuration.add_section('DATABASE')
configuration.set('DATABASE', 'database', 'DBSAInterface')
configuration.set('DATABASE', 'host', 'enzyme.ucd.ie')
configuration.set('DATABASE', 'user', 'peatdb')
configuration.set('DATABASE', 'password', '123')
configuration.writeToFile(self.confpath)
if self.parent != None:
tkMessageBox.showwarning(
"Connection Error",
'No PEATSA server configured, press configure server'
' to set a server, username and password.')
self.connect(configuration)
return
def _doFrame(self):
self.mainwin = self.parent.createChildFrame(width=460,
title='PEATSA Plugin')
#self.mainwin = self.parent.create
methods = self._getmethods()
methods = [m for m in methods if m[0] in self.gui_methods.keys()]
l = Label(self.mainwin, text='PEATSA Interface')
l.pack(side=TOP, fill=BOTH)
self.tf = LabelFrame(self.mainwin, text='Project Calculations')
self.tf.pack(side=TOP, fill=BOTH, expand=1)
self.manageJobsButtons(self.mainwin)
self._createButtons(methods)
self.log = self.createLogWin(self.mainwin)
self.log.pack(side=TOP, fill=BOTH, expand=1)
self.stdout2Log()
self.mainwin.bind("<Destroy>", self.quit)
#self.parent.sidepane.bind("<Destroy>", self.test1)
return
def _createButtons(self, methods):
"""Dynamically create buttons for supplied methods, which is a tuple
of (method name, label)"""
mbutton = Menubutton(self.mainwin,
text='Options',
width=12,
borderwidth=2,
relief=RIDGE,
activeforeground='red')
menu = Menu(mbutton, tearoff=0)
mbutton['menu'] = menu
mbutton.pack(side=BOTTOM, fill=BOTH)
for m in methods:
menu.add_radiobutton(label=self.gui_methods[m[0]],
indicatoron=0,
command=m[1])
b = Button(self.mainwin,
text='Create Calculation',
command=self.createJobDialog)
b.pack(side=BOTTOM, fill=BOTH)
return
def updateJobsTable(self):
"""Show table for current jobs list"""
self.checkJobsDict()
jobdict = self.DB.meta.peatsa_jobs
M = TableModel()
#open job log from file
f = open('jobstates.log', 'r')
jl = pickle.load(f)
for j in jobdict:
jobid = jobdict[j]
try:
M.addRecord(j,
state=jl[jobid]['State'],
date=jl[jobid]['Date'])
except:
M.addRecord(j, state='Not in DB')
self.jobstable = TableCanvas(self.tf,
model=M,
height=100,
editable=False)
self.jobstable.createTableFrame()
self.log.yview('moveto', 1)
f.close()
return
def manageJobsButtons(self, parent):
fr1 = Frame(parent)
Button(fr1,
text='View Results',
command=self.showAllResults,
bg='#ccFFFF').pack(side=TOP, fill=BOTH, expand=1)
fr1.pack(fill=BOTH)
Button(fr1, text='Merge Results',
command=self.mergeCurrent).pack(side=TOP, fill=BOTH, expand=1)
fr1.pack(fill=BOTH)
fr = Frame(parent)
c = '#ADD8E6'
Button(fr, text='Show Details', command=self.viewDetails,
bg=c).pack(side=LEFT, fill=BOTH, expand=1)
Button(fr, text='Manage Results', command=self.manageResults,
bg=c).pack(side=LEFT, fill=BOTH, expand=1)
Button(fr, text='Remove', command=self.removeJob, bg=c).pack(side=LEFT,
fill=BOTH,
expand=1)
Button(fr, text='Resubmit', command=self.resubmitJob,
bg=c).pack(side=LEFT, fill=BOTH, expand=1)
fr.pack(fill=BOTH)
return
def createLogWin(self, parent):
log = Pmw.ScrolledText(parent,
borderframe=1,
labelpos='n',
label_text='Log',
usehullsize=1,
hull_width=800,
hull_height=200,
text_wrap='word')
return log
def stdout2Log(self):
"""Redirect stdout to app control"""
sys.stdout = self
sys.stderr = self
return
def log2Stdout(self):
"""return to stdout"""
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
return
def write(self, txt):
"""Handle stdout if required"""
self.log.appendtext(txt)
self.log.update_idletasks()
return
def flush(self):
return
def connect(self, configuration):
"""Create connection"""
self.connection = PEATSA.WebApp.UtilityFunctions.ConnectionFromConfiguration(
configuration)
self.jobManager = PEATSA.WebApp.Data.JobManager(self.connection)
self.jobManager.setJobStateLogging('jobstates.log', interval=60)
print '\nConnection to server made sucessfully.\n'
return
def createMutationList(self, filename=None):
self.mutationList = Core.Data.MutationListFile(create=False)
return
def fetchJob(self):
"""Get job from it's db ID and add to list"""
mpDlg = MultipleValDialog(title='Get Job',
initialvalues=('', 'my job1'),
labels=(
'ID',
'Your label',
),
types=('string', 'string'),
parent=self.mainwin)
if mpDlg.result == True:
jobid = mpDlg.results[0]
name = mpDlg.results[1]
else:
return
job = PEATSA.WebApp.Data.Job(jobid, self.connection)
if job != None:
print 'adding job id %s to list' % job.identification
self.storeJob(name, job)
self.updateJobs()
return
def writetempPDB(self, name=None, pdbfile='refprot.pdb'):
if name == None:
name = self.DB.meta.refprotein
pdblines = self.DB[name].Structure
#pdbfile = 'refprot.pdb'
fd = open(pdbfile, 'w')
for line in pdblines:
fd.write(line)
fd.close()
return pdbfile
def getrefPDBName(self):
name = self.DB.meta.refprotein
if self.DB[name].has_key('pdbname'):
name = self.DB[name]['pdbname']
return name.split('.')[0]
else:
return ''
def createJobDialog(self):
"""Get details from user using dialog
required: structure, mutations, type of calc and a tag (optional)"""
def validatename(text):
if not hasattr(self.DB.meta, 'peatsa_jobs'):
return 1
if text in self.DB.meta.peatsa_jobs:
return -1
else:
return 1
def close():
jobdlg.destroy()
def loadmuts():
filename = tkFileDialog.askopenfilename(initialdir=os.getcwd(),
filetypes=[("All files",
"*")])
if filename:
mutlist.importfile(filename)
return
def loadmutsfromDB():
for p in self.DB.getRecs():
mut = self.DB.get(p).Mutations
if mut == None or mut == '':
continue
if type(mut) is types.StringType:
mutlist.appendtext(mut + '\n')
else:
mutstring = mut.getMutationString()
if mutstring != None:
mutlist.appendtext(mutstring + '\n')
return
def getstruct():
filename = tkFileDialog.askopenfilename(defaultextension='.pdb',
initialdir=os.getcwd(),
filetypes=[
("pdb", "*.pdb"),
("All files", "*.*")
])
pdbentry.setvalue(filename)
return
def getligand():
self.ligandfile = tkFileDialog.askopenfilename(
defaultextension='.pdb',
initialdir=os.getcwd(),
filetypes=[("mol2", "*.mol2"), ("All files", "*.*")])
def submit():
#if calcmenu.getcurselection() == 'both':
# calcs = ['stability','binding']
if calcmenu.getcurselection() == 'pka':
calcs = ['scan']
else:
calcs = [calcmenu.getcurselection()]
mutationlist = mutlist.getvalue().split('\n')
mutationlist.remove('')
pdbfile = None
pdb = None
quality = mutqualentry.getvalue()
if not hasattr(self.DB.meta,
'refprotein') or self.DB.meta.refprotein == None:
tkMessageBox.showinfo('No ref protein',
'Set a reference (wt) protein first')
return
#if self.useref.get() == 1:
#we use ref pdb by default now
pdbfile = self.writetempPDB()
pdbname = self.getrefPDBName()
if len(mutationlist) == 0 or mutationlist == [u'']:
print 'mutation list is empty'
return
if hasattr(self.DB.meta, 'peatsa_jobs') and nameentry.getvalue(
) in self.DB.meta.peatsa_jobs:
print 'job name already used'
return
name = nameentry.getvalue()
expcol = expcolmenu.getcurselection()
self.submitJob(name=name,
pdbname=pdbname,
pdb=pdb,
pdbfile=pdbfile,
ligandfile=self.ligandfile,
mutations=mutationlist,
calcs=calcs,
mutationquality=quality,
meta={
'expcol': expcol,
'pdbname': pdbname
})
close()
jobdlg = Toplevel()
jobdlg.geometry('+220+220')
jobdlg.title('Create Calculation')
balloon = Pmw.Balloon(jobdlg)
nameentry = Pmw.EntryField(jobdlg,
labelpos='w',
label_text='Name:',
validate=validatename,
value='mycalc')
nameentry.pack(fill=BOTH, expand=1)
balloon.bind(nameentry,
'Calculation name can be anything, but should be unique')
expcols = [''] + self.DB.getSimpleFields()
expcolmenu = Pmw.OptionMenu(jobdlg,
labelpos='w',
label_text='Exp. col:',
items=expcols,
initialitem='',
menubutton_width=8)
expcolmenu.pack(fill=BOTH, expand=1)
balloon.bind(expcolmenu,
'Field with experimental data to compare, optional')
calcmenu = Pmw.OptionMenu(jobdlg,
labelpos='w',
label_text='Calculation Type:',
items=self.calctypes,
initialitem='stability',
menubutton_width=8)
calcmenu.pack(fill=X, expand=1)
fr = Frame(jobdlg)
fr.pack(fill=X, expand=1)
mutqualentry = Pmw.EntryField(jobdlg,
labelpos='w',
label_text='Quality:',
validate=validatename,
value='2.0')
mutqualentry.pack(fill=BOTH, expand=1)
Label(jobdlg,
text='Using PDB: ' + self.getrefPDBName()).pack(fill=BOTH,
expand=1)
self.ligandfile = None
mutlist = Pmw.ScrolledText(jobdlg,
labelpos='n',
label_text='Mutations:',
usehullsize=1,
hull_width=200,
hull_height=250,
text_wrap='word')
mutlist.pack(fill=BOTH, expand=1)
Button(jobdlg,
text='Load Mutations from Project',
command=loadmutsfromDB).pack(fill=X, expand=1)
Button(jobdlg, text='Load Mutations from File',
command=loadmuts).pack(fill=X, expand=1)
balloon.bind(
mutlist,
'Enter one mutation per line in the form\n A:0003:ALA or A3A')
f = Frame(jobdlg)
f.pack(fill=X, expand=1)
Button(f, text='Submit', command=submit).pack(side=LEFT,
fill=X,
expand=1,
pady=2)
Button(f, text='Cancel', command=close).pack(fill=X, expand=1, pady=2)
jobdlg.grab_set()
jobdlg.transient(self.parent)
self.parent.wait_window(jobdlg)
return
def submitJob(self,
name='mycalc',
pdbname=None,
pdb=None,
pdbfile=None,
ligandfile=None,
mutations=[],
calcs=['stability'],
mutationquality='2.0',
meta={}):
"""Submit job to server"""
if 'scan' in calcs and pdbname == None:
print 'You must provide pdb code for pKa calcs'
return
if pdb == None and pdbfile == None:
return
job = self.jobManager.createJob(
pdbId=pdbname,
calculations=calcs,
dataTable='Data',
metadata=meta,
optionArgs={'--mutationQuality': mutationquality})
if pdb != None:
job.setStructure(pdb)
else:
job.setStructureFromFile(pdbfile)
if 'binding' in calcs:
job.setLigandFromFile(ligandfile)
self.mutationList = Core.Data.MutationListFile(filename='tempmutlist',
create=True)
sets = []
for code in mutations:
if code == '': continue
try:
sets.append(Core.Data.MutationSet(code))
except:
print 'mutation code %s incorrect' % code
for s in sets:
self.mutationList.addMutant(s,
autoUpdate=False,
ignoreDuplicates=True)
self.mutationList.removeDuplicates(autoUpdate=False)
job.setMutationListFile(self.mutationList)
job.setState('Ready')
self.jobManager.logJobStates('jobstates.log')
#add job to peat database
self.storeJob(name, job)
if self.parent != None:
username = self.parent.username
self.updateJobs()
else:
username = None
self.DB.commit(note='peatsa job', user=username)
print 'job submitted successfully'
return
def resubmitJob(self):
"""Resend a job based on new mutations in DB that are not in job already"""
job, name = self.getJob()
if job == None:
return
DB = self.DB
self.matrices = job.data.allMatrices()
for m in matrices:
matrix = matrices[m]
if matrix == None: return
muts = matrix.mutationCodes()
dbmuts = [DB.get(p).Mutations for p in DB.getRecs()]
newmuts = list(set(dbmuts) - set(muts))
print 'the following mutations in the project are not in the job: %s' % newmuts
'''self.submitJob(name=name,
pdb=pdb, pdbfile=pdbfile,
ligandfile=self.ligandfile,
mutations=newmuts,
calcs=calcs, meta={'expcol':expcol}) '''
self.log.yview('moveto', 1)
return
def getJob(self, name=None):
"""Get job from name"""
if name == None:
name = self.jobstable.get_selectedRecordNames()[0]
if name == None:
return None, name
jobid = self.DB.meta.peatsa_jobs[name]
try:
job = PEATSA.WebApp.Data.Job(jobid, self.connection)
except:
#print 'job not in database'
return None, name
return job, name
def removeJob(self):
"""Remove a job from the db"""
job, name = self.getJob()
answer = tkMessageBox.askyesno("Warning", 'Remove this job?')
if answer == False:
return
try:
self.jobManager.deleteJob(job)
except:
print 'job not in database, removing from peat'
del self.DB.meta.peatsa_jobs[name]
self.DB.meta.__p__changed = 1
self.updateJobs()
return
def viewDetails(self, name=None):
job, name = self.getJob()
if job == None:
return
jobmeta = job.metadata()
print
print job.data
print 'details for job %s' % name
print 'job status:', job.state()
print 'submitted on ', job.date
if jobmeta.has_key('pdbname'):
print 'original pdb file:', jobmeta['pdbname']
print 'mutations:', len(job.mutationListFile().mutantList())
print '(this job has id %s)' % job.identification
if job.error() != None:
print 'The job had an error..'
print job.error()['ErrorDescription']
print job.error()['DetailedDescription']
print
self.log.yview('moveto', 1)
return
def addColoredText(self, st, tag, word, fg='black', bg='white'):
"""add a space to the end of the word"""
word = word + " "
st.insert('end', word)
end_index = st.index('end')
begin_index = "%s-%sc" % (end_index, len(word) + 1)
st.tag_add(tag, begin_index, end_index)
st.tag_config(tag, foreground=fg, background=bg)
return
def checkJobsDict(self):
"""Check jobs data structure exists"""
if not hasattr(self.DB.meta, 'peatsa_jobs'):
from ZODB.PersistentMapping import PersistentMapping
self.DB.meta.peatsa_jobs = PersistentMapping()
def storeJob(self, name, job):
"""Store job to DB"""
self.checkJobsDict()
self.DB.meta.peatsa_jobs[name] = job.identification
return
def updateJobs(self):
if not hasattr(self.DB.meta, 'peatsa_jobs'):
return
self.updateJobsTable()
self.wait = self.mainwin.after(60000, self.updateJobs)
return
def mergeResults(self, job, colname, tablemodel):
"""Merge given job results to tablemodel"""
if job == None:
return
matrices = job.data.allMatrices()
if not colname:
return
nf = {'Total': colname}
for m in matrices:
matrix = matrices[m]
if matrix == None: continue
M = self.mergeMatrix(matrix,
tablemodel,
fields=['Total'],
newfields=nf)
return
def mergeCurrent(self):
"""Auto merge selected job results to main table
called from GUI """
job, name = self.getJob()
if job == None:
return
#get field name to use
colname = tkSimpleDialog.askstring("Column name?",
"Name for column:",
initialvalue=name + '_Predictions',
parent=self.mainwin)
M = self.parent.tablemodel
self.mergeResults(job, colname, M)
self.parent.updateTable()
#also send some meta data to peatsa_meta?
'''from Correlation import CorrelationAnalyser
C = CorrelationAnalyser()
cc,rmse = C.getStats(pre,exp)
data.append({'name':p,'rmse':rmse,'cc':cc}) '''
return
def manageResults(self, name=None):
"""Get the results back - we can send the matrix to the main peat
table or put results into a labbook sheet.
Also allow user to merge with an existing table"""
job, name = self.getJob(name)
if job.error() != None:
print 'job had an error, use view details'
elif job.state() == 'Finished':
self.showPEATSAResultsDialog(job, name)
else:
print 'Job is not finished yet.'
return
def editConfigFile(self):
"""Edit config file"""
from PEATDB.textFrame import textFrame
tf = textFrame(parent=self.mainwin, title='PEATSA Conf file')
tf.load_from_file(self.confpath)
self.parent.wait_window(tf.frame)
#reconnect
configuration = Core.Environment.Configuration(filename=self.confpath)
self.connect(configuration)
return
def showPEATSAResultsDialog(self, job, name):
resdlg = Toplevel()
resdlg.geometry('600x450+300+200')
resdlg.title('PEATSA results ' + name)
balloon = Pmw.Balloon(resdlg)
self.currname = name
body = Frame(resdlg)
resdlg.initial_focus = body
body.pack(fill=BOTH, expand=1, padx=5, pady=5)
self.matrices = job.data.allMatrices()
fr = Frame(body)
fr.grid(row=0, column=0, sticky='news', rowspan=2)
for m in self.matrices:
if self.matrices[m] != None:
self.showMatrix(fr, self.matrices[m], m)
self.labboklist = self.parent.labbookSheetsSelector(body)
self.labboklist.grid(row=0, column=1, sticky='news')
bf = Frame(body)
bf.grid(row=1, column=1, sticky='ew')
b = Button(bf,
text='Merge into main table',
command=lambda: self.mergeTable(main=True))
b.pack(fill=X, expand=1)
balloon.bind(b, 'Merge results into main DB table')
b = Button(bf, text='Merge into Selected', command=self.mergeTable)
b.pack(fill=X, expand=1)
balloon.bind(
b,
'Merge results into an existing labbook table by matching the mutations'
)
b = Button(bf, text='Create new table', command=self.send2Labbook)
b.pack(fill=X, expand=1)
balloon.bind(b, 'Send results to a new sheet in the main labbook')
Button(bf, text='Save as CSV', command=self.saveCSV).pack(fill=X,
expand=1)
body.columnconfigure(0, weight=1)
body.rowconfigure(0, weight=1)
return
def showMatrix(self, frame, matrix, label=''):
"""Show matrix in table"""
M = self.matrix2Table(matrix)
mtable = self.showTable(frame, M, label)
return mtable
def showTable(self, frame, model, label=''):
"""Show model in table"""
tf = LabelFrame(frame, text=label)
tf.pack(fill=BOTH, expand=1)
mtable = TableCanvas(tf, model=model, cellwidth=70, editable=False)
mtable.createTableFrame()
return mtable
def mergeTable(self, main=False):
"""Send a matrix to the peat main table or labbook sheet
by merging matching mutations.
Requires that one field in the table stores compatible
mutant format supported by PEATSA"""
if main == False:
try:
name = self.labboklist.getcurselection()[0]
except:
print 'no name selected'
return
if main == True:
for m in self.matrices:
matrix = self.matrices[m]
if matrix == None: continue
M = self.parent.tablemodel
M = self.mergeMatrix(matrix, M)
self.parent.updateTable()
else:
M = self.DB.getLabbookSheet(name)
for m in self.matrices:
matrix = self.matrices[m]
if matrix == None: continue
M = self.mergeMatrix(matrix, M)
if M != None:
self.DB.createLabbookSheet(name, M)
self.parent.startLabbook('ALL')
return
def send2Labbook(self):
"""Send matrix to selected labbook"""
#get name
cols = [''] + self.DB.getSimpleFields()
DB = self.DB
mpDlg = MultipleValDialog(title='Send to Labbook',
initialvalues=(self.currname, cols),
labels=('table name', 'exp data column'),
types=('string', 'list'),
parent=self.mainwin)
if mpDlg.result == False:
return
name = mpDlg.results[0]
expcol = mpDlg.results[1]
M = DBActions.sendDB2Labbook(DB,
recs=None,
cols=['Mutations', expcol],
name=name)
for m in self.matrices:
matrix = self.matrices[m]
if matrix != None:
M = self.mergeMatrix(matrix, M)
self.DB.createLabbookSheet(name, M)
self.parent.startLabbook('ALL')
return
def saveCSV(self):
"""Save matrix to csv"""
filename = tkFileDialog.asksaveasfilename(defaultextension='.csv',
initialdir=os.getcwd(),
filetypes=[("csv", "*.csv"),
("All files",
"*.*")])
if not filename:
return
for m in self.matrices:
matrix = self.matrices[m]
if matrix != None:
c = matrix.csvRepresentation()
f = open(filename, 'w')
f.write(c)
f.close()
return
def matrix2Table(self, matrix):
"""Creates a table model from a peatsa matrix"""
M = TableModel()
M.addColumn('Mutations')
fields = matrix.columnHeaders()
for f in fields:
M.addColumn(f)
i = matrix.indexOfColumnWithHeader('Mutations')
for row in matrix:
mutationSet = Core.Data.MutationSet(row[i])
code = '+'.join(mutationSet.mutationCodes(reduced=True))
M.addRow(code)
for f in fields:
j = matrix.indexOfColumnWithHeader(f)
if f == 'Mutations':
M.data[code]['Mutations'] = code
else:
M.data[code][f] = str(row[j])
return M
def mergeMatrix(self, matrix, model, fields=None, newfields=None):
"""Merge a peatsa matrix with a table, returns merged tablemodel
tablemodel: input tablemodel
fields: which fields from matrix should be included in merge, default all
newfields: a dict that can map matrix names to new col names
"""
M = self.matrix2Table(matrix)
if fields == None:
fields = M.columnNames
key = 'Mutations'
if not key in model.columnNames:
print 'this table has no mutations column, we cannot merge'
return
i = matrix.indexOfColumnWithHeader(key)
for row in model.reclist:
try:
mset1 = Core.Data.MutationSet(model.data[row][key])
except:
continue
for rec in M.reclist:
try:
mset2 = Core.Data.MutationSet(M.data[rec][key])
except:
continue
if mset1 == mset2:
#add this data to table
for f in fields:
if newfields != None and newfields.has_key(f):
col = newfields[f]
else:
col = f
if not M.data[rec].has_key(f): continue
model.addColumn(col)
try:
model.data[row][col] = float(M.data[rec][f])
except:
model.data[row][col] = M.data[rec][f]
return model
def showAllResults(self):
"""Show results for single or multiple jobs together"""
names = self.jobstable.get_selectedRecordNames()
if len(names) == 1:
ax, mh, x, y = self.showResults()
else:
tx = []
ty = []
import pylab as plt
f = plt.figure(figsize=(8, 8))
ax = f.add_subplot(111)
for n in names:
a, mh, x, y = self.showResults(n,
showtable=False,
ax=ax,
stats=False)
tx.extend(x)
ty.extend(y)
ax.legend()
#add stats for summary
from Correlation import CorrelationAnalyser
C = CorrelationAnalyser()
C.addStats(ax, tx, ty)
f.show()
return
def showResults(self, name=None, showtable=True, ax=None, stats=True):
"""Show results with correlation plot from selected job"""
job, name = self.getJob(name)
if job == None:
print 'job not in DB'
return
if job.state() != 'Finished':
print 'job not finished'
return
self.matrices = job.data.allMatrices()
#print self.matrices['ModellingResults'].csvRepresentation()
jobmeta = job.metadata()
cols = self.DB.getSimpleFields()
expcol = None
expdata = None
#print jobmeta
if jobmeta.has_key('expcol'):
expcol = jobmeta['expcol']
if expcol not in cols and jobmeta.has_key('project'):
#we may have stored the exp data in another project
prjdata = jobmeta['project']
print 'trying to loading exp data from external project(s)'
from PEATDB.Base import PDatabase
from PEATTables import PEATTableModel
tmpdb = PDatabase(**prjdata)
print tmpdb
S = PEATTableModel(tmpdb)
expdata = S.simpleCopy(include=['Mutations'])
print expdata
#if exp column not known then ask user
if expcol == '' or expcol == None:
mpDlg = MultipleValDialog(title='Select Experimental Data',
initialvalues=[cols],
labels=['exp data column:'],
types=['list'],
parent=self.mainwin)
if mpDlg.result == True:
expcol = mpDlg.results[0]
else:
return
for m in self.matrices:
matrix = self.matrices[m]
if matrix == None or not 'Total' in matrix.columnHeaders():
continue
ax, mh, x, y = self.plotMerged(matrix, expcol, expdata, m,
showtable, ax, name, stats)
#need to add this for mousehandler to work.. hack
'''from Correlation import MouseHandler
mh = MouseHandler(ax, labels=expcol, key='Mutations')
mh.connect()'''
return ax, mh, x, y
def plotMerged(self,
matrix,
expcol,
expdata=None,
title='',
showtable=True,
ax=None,
name=None,
stats=True):
"""Merge a set of exp vals with predictions and plot"""
if expdata == None:
expdata = self.parent.tablemodel.simpleCopy(include=['Mutations'])
merged = self.mergeMatrix(matrix, expdata)
x, y, names, muts = merged.getColumns(
['Total', expcol, 'name', 'Mutations'], allowempty=False)
from Correlation import CorrelationAnalyser
C = CorrelationAnalyser()
muts = ['mutation: ' + i for i in muts]
labels = zip(names, muts)
ax, frame, mh = C.plotCorrelation(x,
y,
labels,
title=title,
ylabel=expcol,
ax=ax,
plotname=name,
stats=stats,
err=4)
x = [round(float(i), 2) for i in x]
y = [round(float(i), 2) for i in y]
if showtable == True:
table = self.showTable(frame, merged)
mh.table = table
return ax, mh, x, y
def test(self):
job, name = self.getJob('myjob')
if job.error() != None or job.state() != 'Finished':
return
stabmatrix = job.data.stabilityResults
L = self.DB.getLabbookSheet('myjob')
L = self.mergeMatrix(stabmatrix, L, fields=['name'])
print L.columnNames
#L1 = self.DB.getLabbookSheet('myjob3')
#L.merge(L1)
return
def displayNoDBWarning(self):
"""Warn user that no DB is present"""
tkMessageBox.showwarning(
"Cannot launch plugin", 'No Database is currently open. '
'You should first open a project.')
return
def help(self):
import webbrowser
link = 'http://enzyme.ucd.ie/main/index.php/PEAT_SA'
webbrowser.open(link, autoraise=1)
return
def quit(self, evt=None):
"""We MUST stop the jobManager"""
self.log2Stdout()
self.jobManager.stopLogging()
self.mainwin.destroy()
print 'closing plugin'
return
def __init__(self, parent=None, model=None, width=300, height=100):
TableCanvas.__init__(self, parent, model, width=width, height=height)
self.parent = parent
return
def createTableFrame(self):
TableCanvas.createTableFrame(self)
self.drawInactive()
return